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WO2011129710A4 - Microarrays - Google Patents

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Publication number
WO2011129710A4
WO2011129710A4 PCT/NZ2011/000052 NZ2011000052W WO2011129710A4 WO 2011129710 A4 WO2011129710 A4 WO 2011129710A4 NZ 2011000052 W NZ2011000052 W NZ 2011000052W WO 2011129710 A4 WO2011129710 A4 WO 2011129710A4
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WO
WIPO (PCT)
Prior art keywords
microarray
dimensional
sample
dimensional microarray
target compound
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Ceased
Application number
PCT/NZ2011/000052
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French (fr)
Other versions
WO2011129710A1 (en
Inventor
Andrew Haynes
Ashton Cyril Partridge
Yinqiu Wu
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Digital Sensing Ltd
Original Assignee
Digital Sensing Ltd
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Priority claimed from AU2010901595A external-priority patent/AU2010901595A0/en
Application filed by Digital Sensing Ltd filed Critical Digital Sensing Ltd
Priority to US13/641,151 priority Critical patent/US20130109585A1/en
Priority to AU2011241208A priority patent/AU2011241208B2/en
Priority to CN201180029536.0A priority patent/CN102971629B/en
Priority to NZ603547A priority patent/NZ603547A/en
Priority to EP11769148.5A priority patent/EP2558859B1/en
Publication of WO2011129710A1 publication Critical patent/WO2011129710A1/en
Publication of WO2011129710A4 publication Critical patent/WO2011129710A4/en
Anticipated expiration legal-status Critical
Priority to US15/967,395 priority patent/US20180327824A1/en
Ceased legal-status Critical Current

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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6813—Hybridisation assays
    • C12Q1/6834—Enzymatic or biochemical coupling of nucleic acids to a solid phase
    • C12Q1/6837—Enzymatic or biochemical coupling of nucleic acids to a solid phase using probe arrays or probe chips
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
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    • B01J19/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J19/0046—Sequential or parallel reactions, e.g. for the synthesis of polypeptides or polynucleotides; Apparatus and devices for combinatorial chemistry or for making molecular arrays
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6813—Hybridisation assays
    • C12Q1/6834—Enzymatic or biochemical coupling of nucleic acids to a solid phase
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
    • G01N33/543—Immunoassay; Biospecific binding assay; Materials therefor with an insoluble carrier for immobilising immunochemicals
    • G01N33/54393—Improving reaction conditions or stability, e.g. by coating or irradiation of surface, by reduction of non-specific binding, by promotion of specific binding
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00277—Apparatus
    • B01J2219/00497—Features relating to the solid phase supports
    • B01J2219/00527—Sheets
    • B01J2219/00531—Sheets essentially square
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00583—Features relative to the processes being carried out
    • B01J2219/00603—Making arrays on substantially continuous surfaces
    • B01J2219/00605—Making arrays on substantially continuous surfaces the compounds being directly bound or immobilised to solid supports
    • B01J2219/00608—DNA chips
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00583—Features relative to the processes being carried out
    • B01J2219/00603—Making arrays on substantially continuous surfaces
    • B01J2219/00605—Making arrays on substantially continuous surfaces the compounds being directly bound or immobilised to solid supports
    • B01J2219/0061—The surface being organic
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00583—Features relative to the processes being carried out
    • B01J2219/00603—Making arrays on substantially continuous surfaces
    • B01J2219/00605—Making arrays on substantially continuous surfaces the compounds being directly bound or immobilised to solid supports
    • B01J2219/00612—Making arrays on substantially continuous surfaces the compounds being directly bound or immobilised to solid supports the surface being inorganic
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00583—Features relative to the processes being carried out
    • B01J2219/00603—Making arrays on substantially continuous surfaces
    • B01J2219/00605—Making arrays on substantially continuous surfaces the compounds being directly bound or immobilised to solid supports
    • B01J2219/00614—Delimitation of the attachment areas
    • B01J2219/00621—Delimitation of the attachment areas by physical means, e.g. trenches, raised areas
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00583—Features relative to the processes being carried out
    • B01J2219/00603—Making arrays on substantially continuous surfaces
    • B01J2219/00605—Making arrays on substantially continuous surfaces the compounds being directly bound or immobilised to solid supports
    • B01J2219/00623—Immobilisation or binding
    • B01J2219/00626—Covalent
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
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    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00583—Features relative to the processes being carried out
    • B01J2219/00603—Making arrays on substantially continuous surfaces
    • B01J2219/00605—Making arrays on substantially continuous surfaces the compounds being directly bound or immobilised to solid supports
    • B01J2219/00632—Introduction of reactive groups to the surface
    • B01J2219/00637—Introduction of reactive groups to the surface by coating it with another layer
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00583—Features relative to the processes being carried out
    • B01J2219/00603—Making arrays on substantially continuous surfaces
    • B01J2219/00659—Two-dimensional arrays

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  • Chemical & Material Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Organic Chemistry (AREA)
  • Engineering & Computer Science (AREA)
  • Immunology (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
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  • Microbiology (AREA)
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  • Medicinal Chemistry (AREA)
  • General Physics & Mathematics (AREA)
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  • Apparatus Associated With Microorganisms And Enzymes (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Sampling And Sample Adjustment (AREA)

Abstract

Disclosed is a method of producing a two dimensional microarray using a three dimensional or structured microarray. The invention involves forming defined functionalized areas by layering an inert material over the surface structures of the three dimensional microarray. Sufficient of the inert material and of the top of the surface structures are then removed to expose defined areas of the surface structures within the inert material.

Claims

AMENDED CLAIMS received by the International Bureau on 10 October 201 1 (10.10.201 1)
1. A method for determining the presence of a target compound(s) of interest within a sample, the method including the steps of: a) Providing a microarray including a plurality of defined functionalized areas, the defined functionalized areas being defined areas having attached sensory agent(s) capable of attaching to the target compound(s) of interest within the sample;
b) Contacting the microarray with at least part of the sample; and
c) Determining the presence of a target compound(s) of interest by detection of a detectable response to the attachment of the target compound(s) to the sensory agent(s).
2. The method of claim 1 wherein the plurality of defined functionalized areas on the microarray, are defined areas on the tops of a plurality of surface structures.
3. The method of claim 1 or 2 wherein the target compound(s) is selected from a micro-organism, a peptide or protein, and/or an antibody.
4. The method of any one of claims 1 to 3 wherein the sensory agent(s) and target compound(s) are, together, biological recognition groups or binding agents.
5. The method of any one of claims 1 to 4 wherein sensory agent(s) and target compound(s) are, together, biological bindings or recognition groups selected from antibody/antigen, DNA/DNA, DNA/protein, protein/protein, protein/receptor, cell/protein and cell/DNA binding partners.
6. The method of any one of the previous claims herein the sample is a tissue sample, a fluid sample, or an oral swab.
7. A method for determining the presence of a target compound(s) of interest within a sample, the method including the steps of: a) Providing a microarray including a plurality of surface structures on a base material, the surface structures having attached sensory agent(s), capable of attaching to the target compound(s) of interest within the sample, on defined functionalized areas on the tops of the surface structures; b) Passing at least part of the sample over the array; and c) Determining the presence of a target compound(s) of interest by detection of a detectable response to the attachment of the target compound(s) to the sensory agent(s).
8. The method of claim 7 wherein the sensory agents and target compounds are, together, biological recognition groups or binding agents.
9. The method of claim 7 or claim 8 wherein sensory agents and target compounds are, together, biological bindings or recognition groups selected from antibody/antigen, DNA/DNA, DNA/protein, protein/protein, protein/receptor, cell/protein and cell/DNA binding partners.
10. The method of any one of claims 2 to 9 wherein the tops of each surface structure includes a defined functionalized area.
11. The method of any one of claims 1 to 10 wherein the microarray includes a plurality of different sensory agents.
12. The method of any one of claims 1 to 11 wherein each defined functionalized area includes a plurality of sensory agents.
13. The method of any one of claims 1 to 12 wherein a signal entity capable of providing a detectable response is attached to the target compound.
14. The method of claim 13 wherein the signal entity is attached to the target compound in the sample prior to step (b), or wherein the signal entity is attached to the target compound between steps (b) and (c).
15. The method of claim 13 or 14 wherein the signal entity is a chemical, biological, or physical entity which is capable of providing a detectable signal or response.
16 The method of claim 15 wherein the signal entity is a particle and is selected from a coloured microbead, a fluorescent microbead, a magnetic microbead, or a light blocking microbead,
17. The method of claim 15 wherein the signal entity is a polymer microbead.
18. The method of claim 17 wherein the polymer microbead is selected from polystyrene beads, PMMA beads and PET beads.
19. T he method of any one of claims 13 to 15 wherein the signal entity includes a synthesized complimentary copy of a single strand of a nucleic acid.
20. The method of any one of claims 1 to 19 wherein the detectable response is selected from colour, fluorescence, light blocking, visual responses, spectrophotometric responses, potentiometric or galvanostatic responses, magnetic light refraction, heat> frequency and digital responses.
21. The method of any one of claims 1 to 20 wherein the detectable response is capable of being read by digital counting, weight measurements, fluorescence, optical, and/or electrical means,
22. The method of any one of claims 1 to 19 wherein the detectable response results in any one or a combination of quantitative/qualitative, fluorescence, optical or colourmetric measurements.
23. The method of any one of claims 1 to 22 wherein the defined functional area is between about 1 nm and 1000 micron in diameter.
24. The method of any one of claims 1 to 23 wherein the defined functional area is the same size or smaller than the size of the signal entity or the target compound.
25. The method of any one of claims 1 to 24 wherein the defined functional areas are separated from each other by about 5 nm to about 20 micron spacing.
26. The method of any one of claims 1 to 25 wherein there are between about 250,000 and about 1 billion defined functional areas per cm2 of the microarray.
The method of any one of claims 1 to 26 wherein the microarray is formed from a plastics material, a metal, a ceramic, an oxide, silicon or a photoresist.
The method of claims 27 wherein the plastics material is selected from PMMA, PET and PS; and the metal is aluminium.
The method of any one of claims 1 to 26 wherein a patterned layer is attached to or formed onto the underside of the microarray to disperse light across the surface where light is passed through the microarray for measurement purposes.
The method of any one of claims 1 to 29 wherein the microarray is formed by etching, lithograph processes, hot embossing, nano-embossing and injection molding or by a Continuous Forming Technology process.
The method of any one of claims 1 to 30 wherein the defined areas are functionaiized using NHa or COOH functional groups.
The method of claim 31 wherein a linker group is attached to the NH2 or COOH functional groups.
The method of claim 32 wherein the linker group is a covalent linker group.
The method of claim 32 or 33 wherein the sensory agent is attached to the linker group.
The method of claim 31 wherein the sensory agent is attached to the NH2 or COOH functional groups.
The method of claims 32 to 34 wherein the linker groups are selected from aliphatic compounds, PEG molecules and polymers, proteins or DNA chains.
The method of claims 1 to 29 wherein the sensory agent is attached directly to the tips of the surface structures through a linker group.
The method of any one of claims 1 to 37 wherein the microarray is coated between the defined functionaiized areas with an inert material.
The method of claim 38 wherein the inert material is selected from gold or silver or chromium, a polymer, or an oil.
40. The method of claim 38 wherein the inert material is a combination of any two metals selected from gold, silver or chromium.
41. The method of claims 38 to 40 wherein the inert material includes a layer of a thiol, protein and/or PEG material to ensure coating adhesion.
42. The method of claims 38 to 41 wherein the microarray includes a secondary inert coating.
43. The method of any one of claims 7 to 42 wherein the sample is a biological sample.
44. The method of claim 43 wherein the biological sample is a tissue sample, a fluid sample, or an oral swab.
45. The method of any one of claims 7 to 44 wherein the target compound is a nucleic acid.
46. The method of any one of claims 7 to 44 wherein the target compound is a biological sample comprising a micro-organism, a peptide or protein, and/or an antibody.
47. A three-dimensional microarray for use in determining the presence of a target compound(s) of interest within a sample, the microarray including: a) a base material including a plurality of surface structures; b) the plurality of surface structures including sensory agent(s) capable of attachment to the target compound(s) of interest within the sample, the sensory agent(s) being included on defined functionalized areas on the tops of each surface structure.
48. The three-dimensional microarray of claim 47 wherein the surface structures are millimeter to nanometer sized surface structures.
49. The three-dimensional microarray of claim 47 or 48 wherein the surface structures are randomly ordered on the surface of the microarray or which are substantially identical and uniformly separated from each other.
The three-dimensional microarray of any one of claims 47 to 49 wherein the surface structures take the form of cones or ridges.
The three-dimensional microarray of any one of claims 47 to 50 wherein the defined functionalized area is between about 1 nm and 1000 micron in diameter.
The three-dimensional microarray of claim 51 wherein the defined functionalized area on the surface structure is between about 1 micron and about 20 micron in diameter.
The three-dimensional microarray of claim 52 wherein the defined functionalized area on the surface structure is between about 5 micron and about 15 micron in diameter.
The three-dimensional microarray of any one of claims 47 to 53 wherein the defined functionalized area is the same size or smaller than the size of the target compound.
The three-dimensional microarray of any one of claims 47 to 54 wherein the defined functionalized areas on the surface structures are separated from each other by about 5 nm to about 20 micron spacing.
The three-dimensional microarray of claim 55 wherein the defined functionalized areas on the surface structures are separated from each other by about 1 to about 20 micron spacing.
The three-dimensional microarray of any one of claims 47 to 56 wherein there are between about 250,000 and about 1 billion defined functionalized areas per cm2.
The three-dimensional microarray of claim 57 wherein there are about 250,000 defined functionalized areas per cm2 at a 10 pm resolution.
The three-dimensional microarray of any one of claims 47 to 58 wherein the microarray is formed from a plastics material, a metal, a ceramic, an oxide, silicon or a photoresist.
60. The three-dimensional microarray of claim 59 wherein the plastics material is selected from PMMA, PET and PS; and the metal is aluminium.
61. The three-dimensional microarray of any one of claims 47 to 58 wherein the microarray is formed from a polymer substrate.
62. The three-dimensional microarray of any one of claims 47 to 60 wherein the base material has a thickness of between about 600 microns and about 2 mm.
63. The three-dimensional microarray of any one of claims 47 to 62 wherein a patterned layer is attached to or formed onto the underside of the base material to disperse light across the surface where light is passed through the microarray for measurement purposes.
64. The three-dimensional microarray of any one of claims 47 to 63 wherein the surface structures are formed by etching, lithographic processes, hot embossing, nano-embossing, injection molding or by the Continuous Forming Technology process as described in WO2007/058548.
66. The three-dimensional microarray of any one of claims 47 to 64 wherein the defined areas are functionalized by NH2 or COOH functional groups.
66. The three-dimensional microarray of any one of claims 47 to 64 wherein the sensory groups are one or more single strands of nucleic acid comprising a promoter region or one more single strands of nucleic acid comprising a specific base sequence of interest.
67. The three-dimensional microarray of claim 65 wherein the sensory groups are one or more single strands of nucleic acid comprising a promoter region or one more single strands of nucleic acid comprising a specific base sequence of interest are attached to the NH2 or COOH functional groups
68. The three-dimensional microarray of claim 65 wherein a linker group is attached to the NH2 or COOH functional groups.
69. The three-dimensional microarray of claim 68 wherein the sensory agent is attached to the linker group.
The three-dimensional microarray of claim 65 wherein a sensory agent is attached to the NH2 or COOH functional groups.
The three-dimensional microarray of claim 68 or 69 wherein the linker group is a covalent linker group.
The three-dimensional microarray of claim 68, 69, or 71 wherein the linker groups are selected from aliphatic compounds, PEG molecules and polymers, proteins or DNA chains.
The three-dimensional microarray of any one of claims 47 to 64 wherein the sensory agent is attached directly to the defined functional ized areas through a linker group.
The three-dimensional microarray of any one of claims 47 to 64 wherein the sensory agents form part of biological recognition groups or binding agents.
The three-dimensional microarray of any one of claims 47 to 64 wherein the sensory agents are selected to attach to the target compounds as part of antibody/antigen, DNA/DNA, DNA/protein, protein/protein, protein/receptor, cell/protein and cell/DNA binding partners.
The three-dimensional microarray of any one of claims 47 to 75 wherein the three-dimensional microarray includes a plurality of sensory agent groupings, each sensory agent grouping forming a section of the microarray.
The three-dimensional microarray of any one of claims 47 to 75 wherein the defined functionalized areas include a plurality of attached sensory agents.
The three-dimensional microarray of any one of claims 47 to 77 wherein the three-dimensional microarray is coated between the defined functionalized areas with an inert material.
The three-dimensional microarray of claim 78 wherein the microarray includes a layer of a thiol, protein or PEG material beneath the inert coating.
The three-dimensional microarray of claim 78 or 79 wherein the inert material is selected from gold or silver or chromium, a polymer or an oil.
81. The three-dimensional microarray of claim 78 or 79 wherein the inert material is a combination of any of gold, silver or chromium.
82. The three-dimensional microarray of any one of claims 78 to 81 wherein the inert material is applied using evaporation, painting, deposition, sputtering, plasma treatment, spray coating, dip coating, or spin coating.
83. The three-dimensional microarray of any one of claims 78 to 82 wherein the microarray includes a secondary inert coating.
84. The three-dimensional microarray of claim 83 wherein the secondary inert coating is a thiol compound.
85. A two-dimensional microarray for use in determining the presence of a target compound(s) of interest within a sample, the microarray including: a) a base material including a plurality of defined functionalized areas; b) the plurality of defined functionalized areas including sensory agent(s) capable of attaching to the target compound(s) of interest within the sample.
Θ6. The two-dimensional microarray of claim 85 wherein the defined functionalized areas are substantially identical in size and uniformly separated from each other or are randomly placed on the surface of the microarra .
87. The two-dimensional microarray of claim 85 or 86 wherein each defined functionalized area is between about 1 nm and 1000 micron in diameter.
88. The two-dimensional microarray of any one of claims 85 to 87 wherein the defined functionalized areas are the same size or smaller than the size of the target compound.
89. The two-dimensional microarray of any one of claims 85 to 88 wherein the defined functionalized areas are separated from each other by about 1 to about 20 micron spacing.
90. The two-dimensional microarray of any one of claims 85 to 89 wherein there are between about 250,000 and about 1 billion defined functionalized areas per cm2.
91. The two-dimensional microarray of any one of claims 85 to 90 wherein the microarray is formed from a polymer substrate; a plastics material, including PMMA, PET or PS; or metals such as aluminium; or ceramics or oxides or silicon or a photoresist or glass.
92. The two-dimensional microarray of any one of claims 85 to 91 wherein the microarray is between about 500 microns and about 2 mm thick.
93. The two-dimensional microarray of any one of claims 85 to 92 wherein a patterned layer is attached to or formed onto the underside of the base material to disperse light across the surface where light is passed through the microarray for measurement purposes.
94. The two-dimensional microarray of any one of claims 85 to 93 wherein the microarray is coated between the defined functionalized areas with an inert material.
95. The two-dimensional microarray of any one of claims 85 to 94 wherein the defined areas are functionalized using NH2 or COOH functional groups, or one or more single strands of nucleic acid comprising a promoter region or one more single strands of nucleic acid comprising a specific base sequence of interest.
96. The two-dimensional microarray of any one of claims 85 to 95 wherein a linker group is attached to the sensory agent.
97. The two-dimensional microarray of claim 96 wherein the linker group is selected from aliphatic compounds, PEG molecules and polymers, proteins or DNA chains.
98. The two-dimensional microarray of any one of claims 85 to 97 wherein the sensory agents form part of a biological recognition group or binding agent.
99. The two-dimensional microarray of any one of claims Θ5 to 98 wherein sensory agents form part of antibody/antigen, DNA/DNA, DNA/protein, protein/protein, protein/receptor, cell/protein and cel!/DNA binding partners.
100. The two-dimensional microarray of any one of claims 85 to 99 wherein the two-dimensional microarray includes a plurality of sensory agent groupings, each sensory agent grouping forming a section of the microarray.
101. The two-dimensional microarray of any one of claims 85 to 100 wherein the defined functionalized areas include a plurality of attached sensory agents.
102. A method of preparing a two dimensional microarray according to claim 85, the method including the steps of forming the defined functionalized areas by layering an inert material between and over the surface structures of a three- dimensional microarray according to claim 47 and then removing sufficient of the inert material and of the top of the surface structures to expose defined areas of the surface structures within the inert material.
103. A method for determining whether or not a nucleic acid comprising a specific sequence of bases is present in a sample, the method comprising: a) in a sample of nucleic acid, where the nucleic acid is double stranded, separating it into single strands;
b) combining the single strands of a nucleic acid with a signal entity conjugate to form a mixed sample;
c) determining whether the nucleic acid comprising a specific sequence of bases is present by running the mixed sample across the surface of a functionalized microarray according to claim 47 or 85; and
d) counting the number of bound signal entity conjugates.
104. A method for determining the extent of methylation in the promoter region of a gene, the said method comprising: a) in a sample of nucleic acid, where the nucleic acid is double stranded, separating it into single strands;
b) treating the sample of nucleic acid such that non-methylated Cytosine is converted to Uracil; c) combining the single strands of nucleic acid with a signal entity conjugate to form a mixed sample;
d) determining the presence and/or extent of methylation in the promoter regions by running the mixed sample across the surface of a functionalized microarray according to claim 47 or 85; and
e) counting the number of bound signal entity conjugates.
105. The method of claim 104 wherein the non-methylated Cytosine bases are converted to Uracil by a chemical conversion using bisulphite.
106. The method according to claims 103, 104, or 105 wherein, the number of bound signal entity conjugates is ascertained by visual techniques, spectrophotometric techniques, fluorescent techniques, potentiometric or galvanostatic techniques, magnetic light refraction, heat, frequency and digital techniques.
107. A method of creating a millimeter to nanometer sized defined area on a surface structure (as herein defined) capable of being functionalised for use as a sensor site, the method including the steps of layering an inert material over the surface structure and then removing sufficient of the inert material from the top of the surface structure to at least partially expose the defined area on the surface structure.
108. A surface structure (as herein defined) for use as millimeter to nanometer sized defined area for use as a sensor site, the surface structure being formed from: i) a base material; and ii) an inert material; wherein the inert material is in a layer over the base material except for the defined area at the top of the surface structure, the defined area being capable of being functionalised to form a sensor site.
109. A three dimensional microarray capable of being functionalised for use in determining the presence of a target compound(s) of interest within a sample, the microarray including a plurality of surface structures according to claim 10Θ.
110. A three-dimensional mlcroarray for use in determining the presence of a target compound(s) of interest within a sample, the microarray including a plurality of surface structures (as herein defined) including a millimeter to nanometer sized defined area for use as a sensor site, wherein an inert material is in a layer on the surface of the base material except for the defined area at the top of the surface structure, and wherein the defined areas include sensory agent(s) capable of attachment to the target compound(s) of interest within the sample.
11 1. A method of creating a millimeter to nanometer sized defined area capable of being functionalised for use as a sensor site, the method including the steps of covering a surface structure (as herein defined) with an inert material and then removing sufficient of the (i) inert material and (ii) the top of the surface structure, to create the defined area on the surface structure within the inert material.
112. A two-dimensional microarray for use in for determining the presence of a target compound(s) of interest within a sample, the two-dimensional structure including a plurality of millimeter to nanometer sized defined areas for use as a sensor site and surrounded by an inert material, the defined areas being capable of being functionalised by inclusion of a sensory agent(s) capable of attachment to the target compound(s) of interest within the sample.
113. A two-dimensional microarray for determining the presence of a target compound(s) of interest within a sample, the two-dimensional microarray including a plurality of surface structures (as herein defined) including millimeter to nanometer sized defined areas for use as a sensor site, wherein an inert material covers the surface structures except for the defined area at the top of the surface structure, and wherein the defined areas include sensory agent(s) capable of attachment to the target compound(s) of interest within the sample.
PCT/NZ2011/000052 2010-04-15 2011-04-15 Microarrays Ceased WO2011129710A1 (en)

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